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Hirak Sarkar

Curriculum Vitae 

hsarkar at  umd.edu | http://www.hiraksarkar.com | @hrksrkr | Google Scholar

Education:

Employment

Bioinformarics Publications:

  1. Hirak Sarkar, Avi Srivastava, Hector Corrada Bravo, Michael I. Love and Rob Patro. "Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data." ISMB 2020
  2. Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro. "A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification." ISMB 2020
  3. Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro. "Alignment and mapping methodology influence transcript abundance estimation." Genome Biology
  4. Hirak Sarkar, Avi Srivastava and Rob Patro. "Minnow: A principled framework for rapid simulation of dscRNA-seq data at the read level" ISMB 2019
  5. Hirak Sarkar*, Mohsen Zakeri*, Laraib Malik and Rob Patro "Towards Selective-Alignment: Producing Accurate And Sensitive Alignments Using Quasi-Mapping" ACM-BCB 2018
  6. Fatemeh Almodaresi*, Hirak Sarkar*, Avi Srivastava and Rob Patro. "An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search" ISMB 2018
  7. Hirak Sarkar and Rob Patro. "Quark enables semi-reference-based compression of RNA-seq data" Bioinfomatics 2017
  8. Avi Srivastava*, Hirak Sarkar*, Laraib Malik and Rob Patro. "Fast, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes" RECOMB-Seq 2016
  9. Avi Srivastava, Hirak Sarkar, Nitish Gupta and Rob Patro. "RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes" ISMB 2016
  10. *~ Co-first author

Other Publications:

  1. Rupak Sarkar, Hirak Sarkar, S Mahinder and AR KhudaBukhsh "Social Media Attributions in the Context of Water Crisis" arXiv:2001.01697
  2. S. Bandyapadhyay, A. Banik, S. Das and H. Sarkar "Voronoi Game on Graphs" WABI 2013, TCS' 2015